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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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next patch: |
| 7 |
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o added tangent linear setup to verification/carbon/ |
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release1_p2 |
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o fixed array boundary problem for adjoint |
| 11 |
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(related to partial recomputation within subroutine |
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related to dynamics -> calc_viscosity -> mom_... |
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o fixed recomputation in thermodynamics |
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o prepare (but not complete) recomputation problem in impldiff |
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o fixed problem for adjoint of global_max |
| 16 |
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o switched off sponge layer code in external_forcing |
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release1_p1 |
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o merged necessary patches: |
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- AD-related changes for GMRedi |
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- fixes i KPP (delZ -> drF) |
| 22 |
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- hook to OBCS songe layer code in external_forcing |
| 23 |
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- errorMessageUnit non-zero in eeboot.F |
| 24 |
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- modified test cost function and carbon verif. |
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release1_chkpt44d_post = chkpt44d_post |
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chkpt44d_pre,post |
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o added missing EXCLUDE_MONITOR flags |
| 30 |
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o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
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(incompatible typ in MIN/MAX expressions caused problems |
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on IBM SP3) |
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o in genmake added variable MAKEDEPEND |
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plus resetting for case SunOS |
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o added timer_stats.c routine for IBM SP3 |
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o removed variables in dynamics |
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o real fresh water flux implemented with non-linear free-surface. |
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chkpt44c_pre,post |
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o few fix (mask in shap_s2, EmPmR in external_field_load, |
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USE_NATURAL_BCS in solve_for_P); |
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o add arguments myIter & myTime to S/R obcs_calc & solve_for_P |
| 44 |
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checkpoint44b_pre/_post |
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o merge of relevant stuff from the ecco-branch: |
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- genmake: removed $S64 overwrite for case SunOS |
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- pkg/exf: update and corrections for field swapping and obcs |
| 49 |
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- pkg/ecco: parameter lists for the_model_main, the_main_loop |
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harmonized between ECCO and MITgcm |
| 51 |
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- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
| 52 |
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updated checkpointing_lev... lists for obcs |
| 53 |
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- model/src: minor changes in forward_step, plot_field |
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added directive for divided adjoint in the_main_loop |
| 55 |
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- pkg/mdsio: added mdsio_gl_slice |
| 56 |
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| 57 |
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o check parameters & config (chkpt44a_pre,post) |
| 58 |
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o OBC and NonLin_FrSurf. |
| 59 |
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checkpoint44 |
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o fix bug in mom_vi_del2uv |
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o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
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o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
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o update AIM experiments (NCEP input files) |
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o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
| 66 |
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o added some stuff for AD |
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checkpoint43 |
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o added two new advection tests |
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o added global 4x4 degree ocean test |
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o added test of H&S94 with free surface on cube |
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o some final mods for gradient check, adjoint,... |
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checkpoint42 |
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Fixed AD-related problems: |
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o Store directives up-to-date with re-arranged Adams-Bashforth |
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(mainly thermodynamics.F) |
| 78 |
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o New store directives for multi-dim. advection schemes |
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* new CPP flag ALLOW_MULTI_DIM_ADVECTION |
| 80 |
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* new common block and key passkey |
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(mainly gad_advection.F) |
| 82 |
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o Modified store directives for split of dynamics/thermodynamics |
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for the case ALLOW_KPP |
| 84 |
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o Cleaned argument list for timestep_tracer.F |
| 85 |
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| 86 |
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checkpoint41 |
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o re-formatted/added comments in prologues of key subroutines |
| 88 |
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to work with protex |
| 89 |
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| 90 |
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checkpoint40 |
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o moved calc_gs, calc_gt and calc_tr1 back to model/src |
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o added FLT (floats) package from Arne along with demo. experiment |
| 93 |
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o re-arranged Adams-Bashforth scheme for tracers to allow easier |
| 94 |
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implementation of forward-in-time forcing terms |
| 95 |
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o more mods for non-linear free-surface including new variable |
| 96 |
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o modified multi-dim method to work on cube |
| 97 |
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o bug fix in KPP (from DM) |
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checkpoint40pre9 |
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o added DST advection schemes |
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o fix MPI bug on SGI's |
| 102 |
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o modifications for non-linear free-surface |
| 103 |
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o fixed conditionals for fixed flow/passive tracer only mode |
| 104 |
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o added tension/strain form of stress tensor |
| 105 |
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o changes to commenting of arguments for TAF/TAMC |
| 106 |
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o added/updated many matlab scripts |
| 107 |
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o added multi-dimensional advection method for tracers |
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checkpoint40pre8 |
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o new package rw/ |
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Added method for dumping intermediate local arrays: |
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mdsio_writetile - same as mdsio_writefield except works from inside |
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bi,bj loop |
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mdsio_writelocal - same as mdsio_writetile except works for local |
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arrays |
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write_local_r? - higher-level wrapper for mdsio_writelocal |
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Controlled by diagFreq. Defaults to zero (ie. no dumps) |
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Example given at end of mom_vecinv.F that dumps some local arrays. |
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o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to |
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control flux-form versus vector invariant code. |
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Switch is runtime flag vectorInvariantMomentum (defaults to false) |
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or genmake -DISABLE ... |
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o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F |
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(additional storing is now needed for case vecinv; |
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currently nothing implemented to switch this storing off |
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in case fluxform is used since no CPP flag available). |
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checkpoint40pre7 |
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o bug fix in dynamics.F |
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calc_viscosity called before k=1,Nr loop. |
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o added some #ifdef's ALLOW_PASSIVE_TRACER |
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o cleaned initialisations in ctrl_map_ini |
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related to TAF |
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checkpoint40pre6 |
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o split dynamics into thermodynamics & dynamics |
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o corresponding split of calc_diffusivity into |
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calc_diffusivity, calc_viscosity |
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(kpp_calc_diff, kpp_calc_visc). |
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o Added diffkr, kapgm to control variables |
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o bug fix in gmredi_slope_limit for ldd97 |
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checkpoint40pre5 |
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o proper initialization of Adams-Bashforth time stepping |
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+ uses forward step for very first step of model (iter=0) |
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o re-generated *all* output since almost all output is modified by this |
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change (sorry but we've been putting this one off for about 2 years) |
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+ natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were |
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*not* regenerated since they are already out of date and I don't |
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want to create the impression that they are suddenly working. |
| 151 |
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o removed KAP stuff for DEC's |
| 152 |
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o modified/added many .cvsignore files in */code and */input |
| 153 |
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o added new expt "solid-body.cs-32x32x1" |
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+ this uses an alternative form of ini_curvilinear_grid.F which |
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is not necessarily any better than the current one... |
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checkpoint40pre4 |
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o added re-initialisations of utrans,vtrans,rtrans in |
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calc_common_factors which are crucial for TAF. |
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o extended iMin,jMin range for calc_common_factors, |
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calc_diffusivity |
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o added option ALLOW_PASSIVE_TRACER |
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o a few minor updates and fixes |
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checkpoint40pre3 |
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o created calc_gtr1.F for gad package |
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o split the_main_loop and re-introduced forward_step |
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o some recomputations of nIter0 for TAMC |
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checkpoint40pre2 |
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o Updated to latest branch of AJA, JMC |
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o Added gradient check package |
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o Added routines for passive tracer handling |
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o Added carbon sequestration sensitivity experiment |
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checkpoint39 |
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o Modifications and fixes to support TAMC |
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(mainly missing or wrong directives) |
| 179 |
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o Corrected common blocks when fooling TAMC to produce adjoint I/O |
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in addummy_in_stepping |
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o Updated verification/vero/ (bug fixes in code/, correct pickups in input/) |
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o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs. |
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o Included following packages: |
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cal: calendar |
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exf: external forcing |
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ecco: essential routines to control use of cal, exf |
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(NB: this is not the full ECCO environment) |
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o disabled some packages by default in genmake |
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checkpoint38 |
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o see notes_c37_adj.txt |
| 192 |
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o corrected wrong layer index in external_forcing_t |
| 193 |
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o replaced the_main_loop/forward_step by the_main_loop |
| 194 |
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o removed forceoutput from write_state |
| 195 |
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(replaced criteria for initial/final state) |
| 196 |
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o added runtime flag for pre-C35 pickups: usePickupBeforeC35 |
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checkpoint37 |
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o mdsio.F routine split and packaged in pkg/mdsio |
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(mdsio.F and mdsio_gl.F still exist in eesupp/src but are not |
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used unless genmake -disable=mdsio) |
| 202 |
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o allow a more precise surface-geopotential gradient for the atmosphere |
| 203 |
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taking into account the change in space of Alpha (=1/rho) at the surface. |
| 204 |
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o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit] |
| 205 |
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(ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa]) |
| 206 |
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o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and |
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Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential |
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[m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere). |
| 209 |
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o Time-Average diagnostics defined as a pseudo package "timeave". |
| 210 |
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o pickup files : old pickup (before c35) did not work with new code (c35 |
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and after) unless activating 2 commented lines in initialise-varia. |
| 212 |
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o Non-Hydrostatic pickup file Pb fixed. |
| 213 |
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o bug with Rigid-lid version (since c35) fixed. |
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checkpoint36 |
| 216 |
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o implement Crank-Nickelson barotropic time-stepping |
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o recover Time-Average diagnostics |
| 218 |
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o fix Pb in checkpoint (PR#19) |
| 219 |
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o AIM become a standard package ; clean unused CPP_kees |
| 220 |
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| 221 |
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checkpoint35 |
| 222 |
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o subtantial rewrite of dynamics.f |
| 223 |
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o allows staggered time-stepping |
| 224 |
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o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt |
| 225 |
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o added bottom drag (linear + quadratic) |
| 226 |
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| 227 |
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checkpoint34 |
| 228 |
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o Modified exchange routines for correct reverse simulation. |
| 229 |
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o Added verification output to comply with bug fix in impldiff.F |
| 230 |
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as of c33 (exp2, natl_box). |
| 231 |
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o Corrected store directives in dynamics.F |
| 232 |
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o Corrected array boundaries in impldiff.F |
| 233 |
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o Corrected array dimensions in gmredi. |
| 234 |
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Added temporary scalars to avoid storage by TAMC (gmredi, kpp). |
| 235 |
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o Added routine GLOBAL_SUM_INT to global_sum.F |
| 236 |
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o Added mdsio_gl.F for ECCO purposes. |
| 237 |
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| 238 |
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checkpoint33 |
| 239 |
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o Fixed bug in lower BC in impldiff.F |
| 240 |
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o Fixed confusion about units of forcing arrays in FFIELDS.h |
| 241 |
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namely Fu,Fv,Qnet,Qsw,EmPmR: |
| 242 |
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- Removed verification/natl_box/code/external_fields_scale.F |
| 243 |
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(did not differ from that in model/src) |
| 244 |
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- Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units |
| 245 |
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(see FFIELDS.h for description) |
| 246 |
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- Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F, |
| 247 |
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kpp_calc.F and kpp_transport_t.F |
| 248 |
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- Removed model/src/external_fields_scale.F and calls to it |
| 249 |
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- verification/natl_box uses flux data with "atmospheric" sign so |
| 250 |
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a special version of external_fields_load.F is used to |
| 251 |
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change the data as it's read in. This way, the arrays |
| 252 |
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have the right units and signs at all times tha a user could |
| 253 |
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possibly use them. |
| 254 |
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o Corrected genmake to delete a temporary file during configuration |
| 255 |
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| 256 |
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checkpoint32 |
| 257 |
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o Scaling of forcing fields moved from external_forcing.F to |
| 258 |
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external_fields_scale.F, called directly after loading fields. |
| 259 |
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o Surface relaxation terms added to surface tendency fields in |
| 260 |
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extra subroutine. |
| 261 |
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o impldiff.F changed to avoid storing by TAMC of huge intermediate |
| 262 |
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fields. |
| 263 |
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o Changes in GMRedi to comply with packaging structure. |
| 264 |
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o Modifications and bug fixes in KPP package. |
| 265 |
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o Verification experiment for KPP added (verification/nat_box/) |
| 266 |
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| 267 |
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checkpoint31 |
| 268 |
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o Packages interface brought in line with defined standard |
| 269 |
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-> new routines packages_...F |
| 270 |
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-> changes in initialise_fixed.F, initialise_varia.F |
| 271 |
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-> enables initialisation interface for ECCO package |
| 272 |
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o Rescaling of external forcing fields immediately after read |
| 273 |
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(removed from external_forcing.F) |
| 274 |
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-> new: surface_fields_scale.F |
| 275 |
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-> affects ini_foorcing.F, external_fields_load.F |
| 276 |
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o Computation of surface tendencies before tendency updates. |
| 277 |
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-> new: external_forcing_surf.F |
| 278 |
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o Change of variable names useGMRedi, useKPP, useECCO |
| 279 |
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o Further changes in dynamics.F, impldiff.F for TAMC |
| 280 |
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o Tested for experiments 0, 2, 4. |
| 281 |
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- not yet tested for GMRedi. |
| 282 |
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- not yet tested for KPP. |
| 283 |
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| 284 |
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checkpoint30 |
| 285 |
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o Updates for OBCs |
| 286 |
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o New experiment for test OBCs (internal_wave) |
| 287 |
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o New output.txt in verification/exp4/results/ |
| 288 |
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o Updates for KPP: calculation of viscosity corrected, new variables |
| 289 |
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kpp_dumpFreq and kpp_taveFreq |
| 290 |
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o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.) |
| 291 |
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and entry for T90 in genmake |
| 292 |
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| 293 |
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checkpoint29 |
| 294 |
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o packaged KPP and GM/Redi |
| 295 |
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| 296 |
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checkpoint28 |
| 297 |
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o Corrected initialization of hFacMin for difference vertical coordinates |
| 298 |
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o Modified calculation of partial cell thickness to more robust algorithm |
| 299 |
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o config_summary.F: replaced write_1D_... by write_0D_... |
| 300 |
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read_write.F: added subroutines write_0D_... |
| 301 |
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o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho: |
| 302 |
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included some initialisations required for TAMC. |
| 303 |
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o routine calc_isoslopes: modified sqrt computation to make it |
| 304 |
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differentiable for zero argument. |
| 305 |
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o routines dynamics, impldiff: |
| 306 |
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included store directives and tape key computations required for TAMC. |
| 307 |
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o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC |
| 308 |
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|
| 309 |
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checkpoint27 |
| 310 |
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o fixed calc_isoslopes() to so that cancellation of terms in tensor |
| 311 |
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formulation works properly with variable resolution. |
| 312 |
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o restructured the calling tree between the_model_main() and dynamics() |
| 313 |
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o split initialise() into initialise_fixed() and initialise_varia() |
| 314 |
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o introduced initialization file pSurfInitFile for free surface (cg2d_x) |
| 315 |
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in new routine ini_psurf() |
| 316 |
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|
| 317 |
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checkpoint26 |
| 318 |
|
o moved some #ifdef in optional routines to encompass everything |
| 319 |
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except the argument declarations. This was using up some memory. |
| 320 |
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o fixed macros like _ADT to work with both versions of Linux cpp |
| 321 |
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o cleaned up some unused and uninitialized variables |
| 322 |
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(helps when debugging with strict compile options) |
| 323 |
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o split up CPP_EEOPTIONS.h into options and macros |
| 324 |
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(macros are now in eesupp/inc/CPP_EEMACROS.h) |
| 325 |
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o patch for 2 processor JAM mode |
| 326 |
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|
| 327 |
checkpoint25 |
checkpoint25 |
| 328 |
o updates for OBCs and NH |
o updates for OBCs and NH |
| 329 |
o dramatically reduced memory usage |
o dramatically reduced memory usage |
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